I just got back from seeing Shrek the Third, and I believe there was a Homestarrunner.com reference in it. I don't know if it was intentional or not, but during Shrek's dream (on the boat) where he's fearing becoming a father, he is engulfed in a wave o' babies. Just thought I'd point out this possible TGS reference.

Yeah, I noticed that and did think that, but I think it's more of a coinky-dink. Now, had Donkey showed up and said "Wave-O-Babies!" then it might mean something, but I think that was just put in to show that Shrek thinks he'll be overwhelmed by being a father with all the babies.